Modification to Fix conversion of Zarr string dataset to HDF5 #1175
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Codecov ReportAll modified and coverable lines are covered by tests ✅
Additional details and impacted files@@ Coverage Diff @@
## fix/zarr_str_export #1175 +/- ##
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+ Coverage 88.83% 88.91% +0.08%
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Files 45 45
Lines 9841 9846 +5
Branches 2798 2797 -1
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+ Hits 8742 8755 +13
+ Misses 779 775 -4
+ Partials 320 316 -4 ☔ View full report in Codecov by Sentry. |
oruebel
reviewed
Aug 27, 2024
| # NOTE: Numpy < 2.0 has only fixed-length strings. | ||
| # Numpy 2.0 introduces variable-length strings (dtype=np.dtypes.StringDType()). | ||
| # HDMF does not yet do any special handling of numpy arrays with variable-length strings. | ||
| if isinstance(value, np.ndarray) or _is_zarr_array(value): |
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The basic approach seems fine. A couple of thoughts:
- I think instead of the
if isinstance(value, np.ndarray) or _is_zarr_array(value)it would be useful to split this case intoifandelifcases to treat numpy and zarr separately here. I think that would be more readable. - I'd move the
_is_zarr_arraymethod ot theutilsordata_utils - Alternatively to this approach we could also use
hasattr(value, filters)to distinguish been Zarr and numpy arrays, because numpy arrays don't have afiltersattribute which is used in Zarr to store all the filters, including the encoder for strings.
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Proposed changes to #1171.
It would be nice if
HDF5IOand theObjectMappercan accept any Zarr array just like it accepts any Numpy array, instead of accepting only Zarr arrays that have been written with hdmf-zarr.